Hello everyone,

I am trying to get Gviz::UcscTrack to display HGNC symbols, or at least the default name from the gene() function. The piece of code I am using is pasted below. Any help is highly appreciated.

ucscGenes <- UcscTrack(genome="hg38", table="ncbiRefSeq", track = 'NCBI RefSeq', trackType="GeneRegionTrack", 
                                   chromosome="chr19", rstarts = "exonStarts", rends = "exonEnds", 
                                   gene = "name", symbol = 'name', transcript = "name", 
                                   strand = "strand", stacking = 'pack', showID = T, geneSymbol = T)

Thank you

The UCSC tables in general don't have the HUGO symbols, so you end up having to add those yourself. But it's really easy to do.

> ucscGenes <- UcscTrack(genome="hg38", table="ncbiRefSeq", track = 'NCBI RefSeq', trackType="GeneRegionTrack",
                                   chromosome="chr19", rstarts = "exonStarts", rends = "exonEnds",
                                   gene = "name", symbol = 'name', transcript = "name",
                                   strand = "strand", stacking = 'pack', showID = T, geneSymbol = T)

> z <- ranges(ucscGenes)

> library(org.Hs.eg.db)

> mcols(z)$symbol <- mapIds(org.Hs.eg.db, gsub("\\.[1-9]$", "", mcols(z)$symbol), "SYMBOL","REFSEQ")
> ucscGenes2 <- ucscGenes
> ranges(ucscGenes2) <- z

> plotTracks(list(ucscGenes, ucscGenes2), chromosome = "chr19", from = 1e6, to = 1.4e6, transcriptAnnotation = "symbol")